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- PDB-6m3f: Crystal structure of the mouse endonuclease EndoG(H138A/C110A), s... -

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Basic information

Entry
Database: PDB / ID: 6m3f
TitleCrystal structure of the mouse endonuclease EndoG(H138A/C110A), space group P212121
ComponentsEndonuclease G, mitochondrial
KeywordsAPOPTOSIS / EndoG / DNase / mitochondria
Function / homology
Function and homology information


mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA nuclease activity / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / negative regulation of TOR signaling / DNA catabolic process ...mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA nuclease activity / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / negative regulation of TOR signaling / DNA catabolic process / response to tumor necrosis factor / positive regulation of autophagy / RNA endonuclease activity / DNA endonuclease activity / perikaryon / in utero embryonic development / nucleic acid binding / mitochondrial inner membrane / positive regulation of apoptotic process / response to antibiotic / DNA damage response / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily
Similarity search - Domain/homology
Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsPark, K.H. / Woo, E.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the mouse endonuclease G.
Authors: Park, K.H. / Yoon, S.M. / Song, H.N. / Yang, J.H. / Ryu, S.E. / Woo, E.J.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endonuclease G, mitochondrial
C: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9944
Polymers54,9462
Non-polymers492
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-45 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.693, 68.880, 127.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endonuclease G, mitochondrial / Endo G


Mass: 27472.879 Da / Num. of mol.: 2 / Mutation: H138A/C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endog / Production host: Escherichia coli (E. coli)
References: UniProt: O08600, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 3350, 0.1M HEPES pH7.5, 0.18M Ammonium sulfate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 9, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 34168 / % possible obs: 90.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.01 / Net I/σ(I): 20.36
Reflection shellResolution: 1.96→2.02 Å / Num. unique obs: 2574 / Rsym value: 0.13

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.96→33.24 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.923
RfactorNum. reflection% reflection
Rfree0.219 1697 4.97 %
Rwork0.169 --
obs0.1714 34168 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.21 Å2
Refinement stepCycle: LAST / Resolution: 1.96→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 0 300 3805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693590
X-RAY DIFFRACTIONf_angle_d0.8464883
X-RAY DIFFRACTIONf_chiral_restr0.0548522
X-RAY DIFFRACTIONf_plane_restr0.0056648
X-RAY DIFFRACTIONf_dihedral_angle_d1.57751712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.020.22061500.17972574X-RAY DIFFRACTION96.56
2.02-2.090.20461300.16592659X-RAY DIFFRACTION98.34
2.09-2.160.23091390.17082671X-RAY DIFFRACTION99.05
2.16-2.250.20691440.16712643X-RAY DIFFRACTION99.08
2.25-2.350.23361270.16552693X-RAY DIFFRACTION99.3
2.35-2.470.19581350.1672671X-RAY DIFFRACTION99.05
2.47-2.630.24041420.17242688X-RAY DIFFRACTION99.68
2.63-2.830.2371420.17932728X-RAY DIFFRACTION99.45
2.83-3.120.23281640.17442694X-RAY DIFFRACTION99.72
3.12-3.570.20111370.16092739X-RAY DIFFRACTION99.76
3.57-4.490.18651290.15332812X-RAY DIFFRACTION99.93
4.49-100.24581580.18262899X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 17.1582277256 Å / Origin y: 6.24538238956 Å / Origin z: 28.8941472579 Å
111213212223313233
T0.127738542251 Å2-0.0114008278991 Å2-0.00622250974085 Å2-0.14233665154 Å2-0.00757367780404 Å2--0.186963487095 Å2
L0.527874586703 °2-0.120194370741 °20.406979162178 °2-0.617335153343 °2-0.338090396628 °2--1.70024260595 °2
S0.00536509301407 Å °0.0384853260204 Å °-0.0460936370007 Å °-0.00591257570484 Å °-0.00815883060585 Å °0.000232976171196 Å °-0.0310178000524 Å °0.0795497956695 Å °0.00514557238946 Å °
Refinement TLS groupSelection details: all

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